Process Description

Allele Specific Expression Filter

The Allele Specific Expression Filter process uses both DNA and RNA intensity data to screen for potential allele-specific expression.

In this filter, log ratios of the intensities of the A allele to the B allele are constructed for each probeset. The intensities from homozygous individuals are used to create a regression model. Each heterozygous SNP is then assessed for Allele Specific Expression using statistical tests based on the observed DNA and RNA ratio intensity against the corresponding expected values from the regression model. The intensities from the heterozygotes are then plotted against the corresponding regression model. Expression patterns that stray from the estimated standard error of the predicted value from the regression model are suggestive of allele-specific expression. Loci exhibiting this pattern can be selected and subjected to further analysis.

Caution: This process can be computationally intensive for large data sets.

Note: This process is considered experimental.

What do I need?

Three data sets are required to run this process:

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A DNA Intensity Input SAS Data Set listing DNA intensity values at the allelic level. The pseudo_dna.sas7bdat data set serves as an example, and is shown below.

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An RNA Intensity Input SAS Data Set listing RNA intensity values at the allelic level. The pseudo_rna.sas7bdat data set serves as an example, and is shown below.

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An Experimental Design SAS Data Set of DNA Intensity. This data set must contain the corresponding experimental design information for the DNA Intensity Input SAS Data Set. Each row of this data set must correspond to a column in the DNA Intensity Input SAS Data Set. One column must be named ColumnName, and its values must exactly match the column names in the DNA Intensity Input SAS Data Set. The exp_dna.sas7bdat data set serves as an example, and is shown below.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

The output generated by this process is summarized in a Tabbed report. Refer to the Allele Specific Expression Filter output documentation for detailed descriptions and guides to interpreting your results.